comparison coverageBed.xml @ 45:a1a923cd89e8 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit d1ee301a39e9830693eedb6ca089456081540f28

44:589e7e57fd6d

<tool id="bedtools_coveragebed" name="bedtools Compute both the depth and breadth of coverage" version="@TOOL_VERSION@" profile="@PROFILE@">
    <description>of features in file B on the features in file A (bedtools coverage)</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools" />

bedtools coverage
$d
$hist
$split
$strandedness
#if str($overlap_a):
    -f $overlap_a
#end if
#if str($overlap_b):
    -F $overlap_b

            label="Report the depth at each position in each A feature"
            help="Positions reported are one based. Each position and depth follow the complete B feature" />
        <param argument="-hist" type="boolean" truevalue="-hist" falsevalue="" checked="false"
            label="Report a histogram of coverage for each feature in A as well as a summary histogram for all features in A"
            help="Additional columns after each feature in A: 1) depth 2) # bases at depth 3) size of A 4) % of A at depth" />
        <expand macro="overlap" name="overlap_a" />
        <expand macro="overlap" name="overlap_b" argument="-F" fracof="B" />
        <param name="reciprocal_overlap" argument="-r" type="boolean" truevalue="-r" falsevalue="" checked="false"
            label="Require that the fraction overlap be reciprocal for A AND B."
            help="if -f is 0.90 and -r is used, this requires that B overlap 90% of A and A _also_ overlaps 90% of B" />

        <test>
            <param name="inputA" value="coverageBedA2.bed" ftype="bed" />
            <param name="inputB" value="coverageBed.bam" ftype="bam" />
            <output name="output" file="coverageBed_result5_unsorted.bed" ftype="bed" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

`bedtools coverage`_ computes both the *depth* and *breadth* of coverage of features in

45:a1a923cd89e8

<tool id="bedtools_coveragebed" name="bedtools Compute both the depth and breadth of coverage" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
    <description>of features in file B on the features in file A (bedtools coverage)</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools" />

bedtools coverage
$d
$hist
$split
$strandedness
$mean
#if str($overlap_a):
    -f $overlap_a
#end if
#if str($overlap_b):
    -F $overlap_b

            label="Report the depth at each position in each A feature"
            help="Positions reported are one based. Each position and depth follow the complete B feature" />
        <param argument="-hist" type="boolean" truevalue="-hist" falsevalue="" checked="false"
            label="Report a histogram of coverage for each feature in A as well as a summary histogram for all features in A"
            help="Additional columns after each feature in A: 1) depth 2) # bases at depth 3) size of A 4) % of A at depth" />
        <param name="mean" argument="-mean" type="boolean" label="Mean depth" truevalue="-mean" falsevalue="" checked="false"
            help="Report the mean depth of all positions in each A feature."/>
        <expand macro="overlap" name="overlap_a" />
        <expand macro="overlap" name="overlap_b" argument="-F" fracof="B" />
        <param name="reciprocal_overlap" argument="-r" type="boolean" truevalue="-r" falsevalue="" checked="false"
            label="Require that the fraction overlap be reciprocal for A AND B."
            help="if -f is 0.90 and -r is used, this requires that B overlap 90% of A and A _also_ overlaps 90% of B" />

        <test>
            <param name="inputA" value="coverageBedA2.bed" ftype="bed" />
            <param name="inputB" value="coverageBed.bam" ftype="bam" />
            <output name="output" file="coverageBed_result5_unsorted.bed" ftype="bed" />
        </test>
        <test>
            <param name="inputA" value="coverageBedA2.bed" ftype="bed" />
            <param name="inputB" value="coverageBed.bam" ftype="bam" />
            <param name="mean" value="true"/>
            <output name="output" file="mean_coverage.bed" ftype="bed" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

`bedtools coverage`_ computes both the *depth* and *breadth* of coverage of features in